DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease

Abstract

DNA methylation is a major determinant in the epigenetic silencing of genes. The mechanisms underlying the targeting of DNA methylation and the subsequent repression of transcription are relevant to human development and disease, as well as for attempts at somatic gene therapy. The success of transgenic technologies in plants and animals is also compromised by DNA methylation-dependent silencing pathways. Recent biochemical experiments provide a mechanistic foundation for understanding the influence of DNA methylation on transcription. The DNA methyltransferase Dnmt1, and several methyl-CpG binding proteins, MeCP2, MBD2, and MBD3, all associate with histone deacetylase. These observations firmly connect DNA methylation with chromatin modifications. They also provide new pathways for the potential targeting of DNA methylation to repressive chromatin as well as the assembly of repressive chromatin on methylated DNA. Here we discuss the implications of the methylation-acetylation connection for human cancers and the developmental syndromes Fragile X and Rett, which involve a mistargeting of DNA methylation-dependent repression.

Figure 1

GAL4-VP16 fails to activate transcription from the methylated and chromatinized HSV tk promoter. The effect of overexpressed GAL4-VP16 on transcription was assayed as indicated. RNA encoding GAL4-VP16 was injected either before (lanes 1–4) or after (lanes 5–8) chromatin assembly of methylated (lanes 1, 2, 5, 6) or unmethylated (lanes 3, 4, 7, 8) plasmid pG5-HSVtk, as indicated. Transcriptional activity was assayed by primer extension as before. Co-injection of pCMVCAT (0.25 ng per oocyte) serves as an internal standard [see (55) for details of a similar experiment].

Figure 2

The Mi-2 complex can be targeted by DNA bound repressors, or by DNA methylation, or by the two in combinantion. Once recruited the Mi-2 complex uses the energy of ATP hydrolysis to disrupt chromatin and facilitate histone deacetylation.

Figure 3

A model for roles of RbAp48-associated proteins during chromatin assembly. Rbp48 is a component of (a) a cytoplasmic histone acetyltransferase with hat1p; (b) a chromatin assembly factor with CAF1; and (c) a histone deacetylase HDAC. Depending on the subunit composition, this protein will be variously equipped to contribute to all these functions in which the modification state of H4, its cellular localization and deposition in a nucleosome, will change as indicated. In all instances shown here the RbAp48–HDAC complex interacts with subnucleosomal particles. The transition between (b) and (c) represents chromatin maturation on nascent DNA following replication.

Figure 4

RbAp48 and HDAC are also components of the nucleosomal ATPase Mi-2 complex. (a) Active chromatin has transcriptionally engaged RNA polymerase II and the basal transcriptional machinery. Under these conditions the core histones in nucleosomes are hyperace-tylated. (b) A DNA binding transcriptional repression recruits the Mi-2 complex. The nucleosomal ATPase disrupts the acetylated nucleoso-mal infrastructure to facilitate RbAp48 access to H4 and histone deacetylation. As a consequence transcription is repressed.